Vertical flow filters are containers filled with porous medium that are recharged from top and drained at the bottom, and are operated at partly saturated conditions. They have recently been suggested as treatment technology for groundwater containing volatile organic compounds (VOCs). Numerical reactive transport simulations were performed to investigate the relevance of different filter operation modes on biodegradation and/or volatilization of the contaminants and to evaluate the potential limitation of such remediation mean due to volatile emissions. On the basis of the data from a pilot-scale vertical flow filter intermittently fed with domestic waste water, model predictions on the system’s performance for the treatment of contaminated groundwater were derived. These simulations considered the transport and aerobic degradation of ammonium and two VOCs, benzene and methyl tertiary butyl ether (MTBE). In addition, the advective-diffusive gas-phase transport of volatile compounds as well as oxygen was simulated. Model predictions addressed the influence of depth and frequency of the intermittent groundwater injection, degradation rate kinetics, and the composition of the filter material. Simulation results show that for unfavorable operation conditions significant VOC emissions have to be considered and that operation modes limiting VOC emissions may limit aerobic biodegradation. However, a suitable combination of injection depth and composition of the filter material does facilitate high biodegradation rates while only little VOC emissions take place. Using such optimized operation modes would allow using vertical flow filter systems as remediation technology suitable for groundwater contaminated with volatile compounds.